def test_defaultExt():
fslOutputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ']
exts = ['.nii', '.img', '.nii.gz']
os.environ.pop('FSLOUTPUTTYPE', None)
assert fslimage.defaultExt() == '.nii.gz'
for o, e in zip(fslOutputTypes, exts):
os.environ['FSLOUTPUTTYPE'] = o
assert fslimage.defaultExt() == e
def prepIn(workdir, name, val):
infile = None
if isinstance(val, fslimage.Image):
intypes.append(fslimage.Image)
elif isinstance(val, nib.nifti1.Nifti1Image):
intypes.append(nib.nifti1.Nifti1Image)
if isinstance(val, fslimage.Image):
val = val.nibImage
if isinstance(val, nib.nifti1.Nifti1Image):
infile = val.get_filename()
# in-memory image - we have
# to save it out to a file
if infile is None or not op.exists(infile):
hd, infile = tempfile.mkstemp(fslimage.defaultExt(),
dir=workdir)
os.close(hd)
# Create a copy of the input image and
# save that, so the original doesn't
# get associated with the temp file
val = nib.nifti1.Nifti1Image(
np.asanyarray(val.dataobj), None, val.header)
val.to_filename(infile)
return infile
def test_defaultExt():
fslOutputTypes = [
'NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', 'NIFTI_PAIR_GZ', 'NIFTI2',
'NIFTI2_PAIR', 'NIFTI2_GZ', 'NIFTI2_PAIR_GZ'
]
exts = ['.nii', '.img', '.nii.gz', '.img.gz'] * 2
env = os.environ.copy()
env.pop('FSLOUTPUTTYPE', None)
with mock.patch('os.environ', env):
assert fslimage.defaultExt() == '.nii.gz'
for o, e in zip(fslOutputTypes, exts):
env['FSLOUTPUTTYPE'] = o
assert fslimage.defaultExt() == e
def test_addExt():
"""Test the addExt function. """
default = fslimage.defaultExt()
testdir = tempfile.mkdtemp()
toCreate = [
'compressed.nii.gz', 'uncompressed.nii', 'img_hdr_pair.img',
'compressed_img_hdr_pair.img.gz', 'ambiguous.nii', 'ambiguous.nii.gz',
'ambiguous.img', 'ambiguous.img.gz'
]
# (file, mustExist, expected)
tests = [('blah', False, 'blah{}'.format(default)),
('blah.nii', False, 'blah.nii'),
('blah.nii.gz', False, 'blah.nii.gz'),
('blah.img', False, 'blah.img'), ('blah.hdr', False, 'blah.hdr'),
('blah.img.gz', False, 'blah.img.gz'),
('blah.hdr.gz', False, 'blah.hdr.gz'),
('compressed', True, 'compressed.nii.gz'),
('compressed.nii.gz', True, 'compressed.nii.gz'),
('uncompressed', True, 'uncompressed.nii'),
('uncompressed.nii', True, 'uncompressed.nii'),
('img_hdr_pair', True, 'img_hdr_pair.hdr'),
('img_hdr_pair.hdr', True, 'img_hdr_pair.hdr'),
('img_hdr_pair.img', True, 'img_hdr_pair.img'),
('compressed_img_hdr_pair', True,
'compressed_img_hdr_pair.hdr.gz'),
('compressed_img_hdr_pair.img.gz', True,
'compressed_img_hdr_pair.img.gz'),
('compressed_img_hdr_pair.hdr.gz', True,
'compressed_img_hdr_pair.hdr.gz'),
('ambiguous.nii', True, 'ambiguous.nii'),
('ambiguous.nii.gz', True, 'ambiguous.nii.gz'),
('ambiguous.img', True, 'ambiguous.img'),
('ambiguous.hdr', True, 'ambiguous.hdr'),
('ambiguous.img.gz', True, 'ambiguous.img.gz'),
('ambiguous.hdr.gz', True, 'ambiguous.hdr.gz')]
for path in toCreate:
path = op.abspath(op.join(testdir, path))
make_random_image(path)
try:
for path, mustExist, expected in tests:
path = op.abspath(op.join(testdir, path))
expected = op.abspath(op.join(testdir, expected))
assert fslimage.addExt(path, mustExist) == expected
# Make sure that an ambiguous path fails
with pytest.raises(fslimage.PathError):
path = op.join(testdir, 'ambiguous')
fslimage.addExt(path, mustExist=True)
finally:
shutil.rmtree(testdir)
def reg_bbr(wsp):
"""
Perform BBR registration
:param reg_img: Data to register, e.g. PWI or calibration image. Normally would be brain extracted
:param struc_img: Structural image
:param struc_brain_img: Brain-extracted structural image
Optional keyword arguments:
:param inweight:
:param init: Initial transform matrix
Optional keyword arguments for fieldmap distortion correction:
:param fmap: Fieldmap image
:param fmapmag: Fieldmap magnitude image
:param fmapmagbrain: Fieldmap magnitude image - brain extracted
:param pedir: Phase encoding direction (x, -x, y, -y, z, -z)
:param echospacing: Echo spacing
:return Tuple of registered image, transform matrix
"""
struc.segment(wsp)
wsp.log.write(" - BBR registration using epi_reg...")
# Windows can't run epi_reg as it's a batch script. Use our experimental python
# implementation but use the standard epi_reg on other platforms until the python
# version is better tested
if sys.platform.startswith("win"):
import oxasl.epi_reg as pyepi
result = pyepi.epi_reg(wsp, wsp.reg.nativeref)
else:
result = epi_reg(epi=wsp.reg.nativeref,
t1=wsp.structural.struc,
t1brain=wsp.structural.brain,
out=fsl.LOAD,
wmseg=wsp.structural.wm_seg,
init=wsp.reg.asl2struc,
inweight=wsp.inweight,
log=wsp.fsllog)
wsp.log.write(" DONE\n")
return result["out%s" % defaultExt()], result["out"]
def prepIn(workdir, name, val):
infile = None
if isinstance(val, fslimage.Image):
intypes.append(fslimage.Image)
elif isinstance(val, nib.nifti1.Nifti1Image):
intypes.append(nib.nifti1.Nifti1Image)
if isinstance(val, fslimage.Image):
val = val.nibImage
if isinstance(val, nib.nifti1.Nifti1Image):
infile = val.get_filename()
# in-memory image - we have
# to save it out to a file
if infile is None:
hd, infile = tempfile.mkstemp(fslimage.defaultExt())
os.close(hd)
val.to_filename(infile)
return infile
def saveOverlay(overlay, display=None):
"""Saves the currently selected overlay (only if it is a :class:`.Image`),
by a call to :meth:`.Image.save`. If a ``display`` is provided, the
:attr:`.Display.name` may be updated to match the new overlay file name.
:arg overlay: The :class:`.Image` overlay to save
:arg display: The :class:`.Display` instance associated with the overlay.
"""
import wx
# TODO support for other overlay types
if not isinstance(overlay, fslimage.Image):
raise RuntimeError('Non-volumetric types not supported yet')
# If this image has been loaded from a file,
# ask the user whether they want to overwrite
# that file, or save the image to a new file.
#
if overlay.dataSource is not None:
# If the data source is not nifti (e.g.
# mgz), we are not going to overwrite it,
# so we don't ask.
if fslimage.looksLikeImage(overlay.dataSource):
msg = strings.messages['SaveOverlayAction.overwrite'].format(
overlay.dataSource)
title = strings.titles['SaveOverlayAction.overwrite'].format(
overlay.dataSource)
dlg = wx.MessageDialog(wx.GetTopLevelWindows()[0],
message=msg,
caption=title,
style=(wx.ICON_WARNING | wx.YES_NO
| wx.CANCEL | wx.NO_DEFAULT))
dlg.SetYesNoCancelLabels(
strings.labels['SaveOverlayAction.overwrite'],
strings.labels['SaveOverlayAction.saveNew'],
strings.labels['SaveOverlayAction.cancel'])
response = dlg.ShowModal()
# Cancel == cancel the save
# Yes == overwrite the existing file
# No == save to a new file (prompt the user for the file name)
if response == wx.ID_CANCEL:
return
if response == wx.ID_YES:
doSave(overlay)
return
fromDir = op.dirname(overlay.dataSource)
filename = fslimage.removeExt(op.basename(overlay.dataSource))
filename = '{}_copy'.format(filename)
else:
fromDir = fslsettings.read('loadSaveOverlayDir', os.getcwd())
if display is not None: filename = display.name
else: filename = overlay.name
filename = filename.replace('/', '_')
filename = filename.replace('\\', '_')
# Ask the user where they
# want to save the image
msg = strings.titles['SaveOverlayAction.saveFile']
dlg = wx.FileDialog(wx.GetApp().GetTopWindow(),
message=msg,
defaultDir=fromDir,
defaultFile=filename,
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() != wx.ID_OK:
return
# Make sure that the user chose a supported
# extension. If not, use the default extension.
savePath = dlg.GetPath()
prefix, suffix = fslimage.splitExt(savePath)
if suffix == '':
savePath = '{}{}'.format(prefix, fslimage.defaultExt())
oldPath = overlay.dataSource
saveDir = op.dirname(savePath)
if doSave(overlay, savePath):
# Cache the save directory for next time.
fslsettings.write('loadSaveOverlayDir', saveDir)
# If image was in memory, or its old
# name equalled the old datasource
# base name, update its name.
if oldPath is None or \
fslimage.removeExt(op.basename(oldPath)) == overlay.name:
overlay.name = fslimage.removeExt(op.basename(savePath))
if display is not None:
display.name = overlay.name
def imcp(src,
dest,
overwrite=False,
useDefaultExt=False,
move=False):
"""Copy the given ``src`` file to destination ``dest``.
A :class:`.fsl.utils.path.PathError` is raised if anything goes wrong.
:arg src: Path to copy. If ``allowedExts`` is provided,
the file extension can be omitted.
:arg dest: Destination path. Can be an incomplete file
specification (i.e. without the extension), or a
directory.
:arg overwrite: If ``True`` this function will overwrite files that
already exist. Defaults to ``False``.
:arg useDefaultExt: Defaults to ``False``. If ``True``, the destination
file type will be set according to the default
extension, specified by
:func:`~fsl.data.image.defaultExt`. If the source
file does not have the same type as the default
extension, it will be converted. If ``False``, the
source file type is not changed.
:arg move: If ``True``, the files are moved, instead of being
copied. See :func:`immv`.
"""
import nibabel as nib
if op.isdir(dest):
dest = op.join(dest, op.basename(src))
srcBase, srcExt = fslimage.splitExt(src)
destBase, destExt = fslimage.splitExt(dest)
# src was specified without an
# extension, or the specified
# src does not have an allowed
# extension.
if srcExt == '':
# Try to resolve the specified src
# path - if src does not exist, or
# does not have an allowed extension,
# addExt will raise an error
src = fslimage.addExt(src, mustExist=True)
# We've resolved src to a
# full filename - split it
# again to get its extension
srcBase, srcExt = fslimage.splitExt(src)
if not op.exists(src):
raise fslpath.PathError('imcp error - source path '
'does not exist: {}'.format(src))
# Figure out the destination file
# extension/type. If useDefaultExt
# is True, we use the default
# extension. Otherwise, if no
# destination file extension is
# provided, we use the source
# extension.
if useDefaultExt: destExt = fslimage.defaultExt()
elif destExt == '': destExt = srcExt
# Resolve any file group differences
# e.g. we don't care if the src is
# specified as file.hdr, and the dest
# is specified as file.img - if src
# and dest are part of the same file
# group, we replace the dest extension
# with the src extension.
if srcExt != destExt:
for group in fslimage.FILE_GROUPS:
if srcExt in group and destExt in group:
destExt = srcExt
break
dest = destBase + destExt
# Give up if we don't have permission.
if not os.access(op.dirname(dest), os.W_OK | os.X_OK):
raise fslpath.PathError('imcp error - cannot write to {}'.format(dest))
if move and not os.access(op.dirname(src), os.W_OK | os.X_OK):
raise fslpath.PathError('imcp error - cannot move from {}'.format(src))
# If the source file type does not
# match the destination file type,
# we need to perform a conversion.
#
# This is more expensive in terms of
# io and cpu, but programmatically
# very easy - nibabel does all the
# hard work.
if srcExt != destExt:
if not overwrite and op.exists(dest):
raise fslpath.PathError('imcp error - destination already '
'exists ({})'.format(dest))
img = nib.load(src)
nib.save(img, dest)
if move:
os.remove(src)
return
# Otherwise we do a file copy. This
# is actually more complicated than
# converting the file type due to
# hdr/img pairs ...
#
# If the source is part of a file group,
# e.g. src.img/src.hdr), we need to copy
# the whole set of files. So here we
# build a list of source files that need
# to be copied/moved. The getFileGroup
# function returns all other files that
# are associated with this file (i.e.
# part of the same group).
#
# We store the sources as separate
# (base, ext) tuples, so we don't
# have to re-split when creating
# destination paths.
#
# The unambiguous flag tells getFileGroup
# to raise an error if the source appears
# to be part of an incopmlete file group
# (e.g. file.hdr without an accompanying
# file.img).
copySrcs = fslpath.getFileGroup(src,
fslimage.ALLOWED_EXTENSIONS,
fslimage.FILE_GROUPS,
fullPaths=False,
unambiguous=True)
copySrcs = [(srcBase, e) for e in copySrcs]
# Build a list of destinations for each
# copy source - we build this list in
# advance, so we can fail if any of the
# destinations already exist. We also
# re-combine the source bases/extensions.
copyDests = [destBase + e for (b, e) in copySrcs]
copySrcs = [b + e for (b, e) in copySrcs]
# Fail if any of the destination
# paths already exist
if not overwrite and any([op.exists(d) for d in copyDests]):
raise fslpath.PathError('imcp error - a destination path already '
'exists ({})'.format(', '.join(copyDests)))
# Do the copy/move
for src, dest in zip(copySrcs, copyDests):
if move: shutil.move(src, dest)
else: shutil.copy(src, dest)